Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

Electrical stress and acid orange 7 synergistically clear the blockage of electron flow in the methanogenesis of low-strength wastewater

Energy recovery from low-strength wastewater through anaerobic methanogenesis is constrained by limited substrate availability. The development of efficient methanogenic communities is critical but challenging. Here we develop a strategy to acclimate methanogenic communities using conductive carrier (CC), electrical stress (ES), and Acid Orange 7 (AO7) in a modified biofilter. The synergistic integration of CC, ES, and AO7 precipitated a remarkable 72-fold surge in methane production rate compared to the baseline. This increase was attributed to an altered methanogenic community function, independent of the continuous presence of AO7 and ES. AO7 acted as an external electron acceptor, accelerating acetogenesis from fermentation intermediates, restructuring the bacterial community, and enriching electroactive bacteria (EAB). Meanwhile, CC and ES orchestrated the assembly of the archaeal community and promoted electrotrophic methanogens, enhancing acetotrophic methanogenesis electron flow via a mechanism distinct from direct electrochemical interactions. The collective application of CC, ES, and AO7 effectively mitigated electron flow impediments in low-strength wastewater methanogenesis, achieving an additional 34% electron recovery from the substrate. This study proposes a new method of amending anaerobic digestion systems with conductive materials to advance wastewater treatment, sustainability, and energy self-sufficiency.

Optimization of microbial fuel cell performance application to high sulfide industrial wastewater treatment by modulating microbial function

Microbial fuel cells (MFCs) are innovative eco-friendly technologies that advance a circular economy by enabling the conversion of both organic and inorganic substances in wastewater to electricity. While conceptually promising, there are lingering questions regarding the performance and stability of MFCs in real industrial settings. To address this research gap, we investigated the influence of specific operational settings, regarding the hydraulic retention time (HRT) and organic loading rate (OLR) on the performance of MFCs used for treating sulfide-rich wastewater from a canned pineapple factory. Experiments were performed at varying hydraulic retention times (2 days and 4 days) during both low and high seasonal production. Through optimization, we achieved a current density generation of 47±15 mA/m2, a COD removal efficiency of 91±9%, and a sulfide removal efficiency of 86±10%. Microbiome analysis revealed improved MFC performance when there was a substantial presence of electrogenic bacteria, sulfide-oxidizing bacteria, and methanotrophs, alongside a reduced abundance of sulfate-reducing bacteria and methanogens. In conclusion, we recommend the following operational guidelines for applying MFCs in industrial wastewater treatment: (i) Careful selection of the microbial inoculum, as this step significantly influences the composition of the MFC microbial community and its overall performance. (ii) Initiating MFC operation with an appropriate OLR is essential. This helps in establishing an effective and adaptable microbial community within the MFCs, which can be beneficial when facing variations in OLR due to seasonal production changes. (iii) Identifying and maintaining MFC-supporting microbes, including those identified in this study, should be a priority. Keeping these microbes as an integral part of the system's microbial composition throughout the operation enhances and stabilizes MFC performance.

Conventional Fossil Fuel Extraction, Associated Biogeochemical Processes, and Topography Influence Methane Groundwater Concentrations in Appalachia

The production of fossil fuels, including oil, gas, and coal, retains a dominant share in US energy production and serves as a major anthropogenic source of methane, a greenhouse gas with a high warming potential. In addition to directly emitting methane into the air, fossil fuel production can release methane into groundwater, and that methane may eventually reach the atmosphere. In this study, we collected 311 water samples from an unconventional oil and gas (UOG) production region in Pennsylvania and an oil and gas (O&G) and coal production region across Ohio and West Virginia. Methane concentration was negatively correlated to distance to the nearest O&G well in the second region, but such a correlation was shown to be driven by topography as a confounding variable. Furthermore, sulfate concentration was negatively correlated with methane concentration and with distance to coal mining in the second region, and these correlations were robust even when considering topography. We hypothesized that coal mining enriched sulfate in groundwater, which in turn inhibited methanogenesis and enhanced microbial methane oxidation. Thus, this study highlights the complex interplay of multiple factors in shaping groundwater methane concentrations, including biogeochemical conversion, topography, and conventional fossil extraction.

Evolution and interaction of microbial communities in mangrove microbial fuel cells and first description of Shewanella fodinae as electroactive bacterium

Understanding exoelectrogenic bacteria mechanisms and their interactions in complex biofilm is critical for the development of microbial fuel cells (MFCs). In this article, assumptions concerning the benefits of the complex sediment microbial community for electricity production were explored with both the complex microbial community and isolates identified as Shewanella. Analysis of the microbial community revealed a strong influence of the sediment community on anodes and electrolytes compared to that of only water. Moreover, while Pelobacteraceae-related genera were dominant in our MFCs instead of Desulfuromonas and Geobacter as usually reported, the electroactive Shewanella algae and Shewanella fodinae were isolated and cultivated from the anodic biofilm. S. fodinae, described for the first time as an electroactive bacterium to the best of our knowledge, led to a maximal current density of 3.6 A/m² set as 0.3 V/SCE in a three-electrode set-up fed with lactate. S. algae, in a complex medium containing several available substrates, showed several preferential oxidative behaviors including a diauxic behavior. In pure culture and under our conditions, S. fodinae and S. algae were not able to use acetate as a sole electron donor. However, their presence in our acetate-fed MFCs and the adaptive behavior of S. algae hint a syntrophic interaction between the bacteria to optimize the use of the substrate in a complex environment.

Microbial methane cycling in sediments of Arctic thermokarst lagoons

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH₄ ) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH₄ concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, lipid biomarkers, and network analysis. We assessed how differences in geochemistry between thermokarst lakes and thermokarst lagoons, caused by the infiltration of sulfate-rich marine water, altered the microbial methane-cycling community. Anaerobic sulfate-reducing ANME-2a/2b methanotrophs dominated the sulfate-rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow and low sulfate concentrations compared to the usual marine ANME habitat. Non-competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of differences in porewater chemistry and depth. This potentially contributed to the high CH₄ concentrations observed in all sulfate-poor sediments. CH₄ concentrations in the freshwater-influenced sediments averaged 1.34 ± 0.98 μmol g^-1 , with highly depleted δ¹³ C-CH₄ values ranging from -89‰ to -70‰. In contrast, the sulfate-affected upper 300 cm of the lagoon exhibited low average CH₄ concentrations of 0.011 ± 0.005 μmol g^-1 with comparatively enriched δ¹³ C-CH₄ values of -54‰ to -37‰ pointing to substantial methane oxidation. Our study shows that lagoon formation specifically supports methane oxidizers and methane oxidation through changes in pore water chemistry, especially sulfate, while methanogens are similar to lake conditions.

Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils

Peatlands are among the largest natural sources of atmospheric methane (CH₄ ) worldwide. Microbial processes play a key role in regulating CH₄ emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH₄ emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi-omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome-metabolome interactions; then explore the competition between methanogens and sulfate-reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO₂ production with temperature. In contrast, the decrease in CH₄ production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait-based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non-limiting sulfate concentrations at 21°C, thereby reducing CH₄ emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low-molecular-weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH₄ emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.

Cross-Feedings, Competition, and Positive and Negative Synergies in a Four-Species Synthetic Community for Anaerobic Degradation of Cellulose to Methane

Complex interactions exist among microorganisms in a community to carry out ecological processes and adapt to changing environments. Here, we constructed a quad-culture consisting of a cellulolytic bacterium (Ruminiclostridium cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic methanogen (Methanosaeta concilii), and a sulfate-reducing bacterium (Desulfovibrio vulgaris). The four microorganisms in the quad-culture cooperated via cross-feeding to produce methane using cellulose as the only carbon source and electron donor. The community metabolism of the quad-culture was compared with those of the R. cellulolyticum-containing tri-cultures, bi-cultures, and mono-culture. Methane production was higher in the quad-culture than the sum of the increases in the tri-cultures, which was attributed to a positive synergy of four species. In contrast, cellulose degradation by the quad-culture was lower than the additive effects of the tri-cultures which represented a negative synergy. The community metabolism of the quad-culture was compared between a control condition and a treatment condition with sulfate addition using metaproteomics and metabolic profiling. Sulfate addition enhanced sulfate reduction and decreased methane and CO₂ productions. The cross-feeding fluxes in the quad-culture in the two conditions were modeled using a community stoichiometric model. Sulfate addition strengthened metabolic handoffs from R. cellulolyticum to M. concilii and D. vulgaris and intensified substrate competition between M. hungatei and D. vulgaris. Overall, this study uncovered emergent properties of higher-order microbial interactions using a four-species synthetic community. IMPORTANCE A synthetic community was designed using four microbial species that together performed distinct key metabolic processes in the anaerobic degradation of cellulose to methane and CO₂. The microorganisms exhibited expected interactions, such as cross-feeding of acetate from a cellulolytic bacterium to an acetoclastic methanogen and competition of H₂ between a sulfate reducing bacterium and a hydrogenotrophic methanogen. This validated our rational design of the interactions between microorganisms based on their metabolic roles. More interestingly, we also found positive and negative synergies as emergent properties of high-order microbial interactions among three or more microorganisms in cocultures. These microbial interactions can be quantitatively measured by adding and removing specific members. A community stoichiometric model was constructed to represent the fluxes in the community metabolic network. This study paved the way toward a more predictive understanding of the impact of environmental perturbations on microbial interactions sustaining geochemically significant processes in natural systems.

Lactate as an effective electron donor in the sulfate reduction: impacts on the microbial diversity

The competition between sulfate-reducing bacteria and methane-producing archaea has a major influence on organic matter removal, as well as the success of sulfidogenic systems. This study investigated the performance of six batch sulfidogenic reactors in response to different COD/sulfate ratios (1.0 and 2.0) and electron donors (cheese whey, ethanol, and sodium lactate) by evaluating the biochemical mechanisms of sulfate reduction, organic matter oxidation, and microbial structure modification. A COD/sulfate ratio of 1.0 resulted in high sulfidogenic activity for all electron donors, thereby achieving a nearly 80% sulfate removal. Lactate provided high sulfate removal rates at COD/sulfate ratios of 1.0 (80%) and 2.0 (90%). A COD/sulfate ratio of 2.0 decreased the sulfate removal rates by 25 and 28% when ethanol and cheese whey were used as substrates. The sulfate-reducing bacteria populations increased using ethanol and lactate at a COD/sulfate ratio of 1.0. Particularly, Desulfovibrio, Clostridium, and Syntrophobacter were predominant. Influent composition and COD/sulfate ratio influenced the relative abundance of the microbial communities. Therefore, controlling these parameters may facilitate the wastewater treatment with high sulfate levels through bacterial activity.

Early-stage response in anaerobic bioreactors due to high sulfate loads: Hydrogen sulfide yield and other organic volatile sulfur compounds as a sign of microbial community modifications

In this work, the early-stage response of six lab-scale biogas bioreactors fed with different amounts of a sulfate-rich organic agro-industrial effluent was investigated. Biogas characterization, gas chromatography selective for sulfur compounds and high-throughput sequencing of 16S rRNA gene were performed. Hydrogen sulfide (H₂S) yield went from transient to steady state in ∼ 2 weeks for all the studied conditions. In addition, volatile sulfur compounds (VSCs), like methanethiol (MeSH) and dimethyl sulfide (DMS), were generated at high sulfate loads. Changes were evidenced in the microbial community structures, with a higher abundance of genes involved in the dissimilatory sulfate-reduction pathway in high loaded sulfate bioreactors, as determined by PICRUSt analysis. Principal component analysis (PCA) and correlation analyses evidenced strong relationships between H₂S, VSCs and the microbial community. Sulfate-reducing bacteria (SRB) like Desulfocarbo, Desulfocella and Desulfobacteraceae might be possibly linked with methylation processes of H₂S.

Antimicrobial and Anticorrosion Activity of a Novel Composite Biocide against Mixed Bacterial Strains in Taiwanese Marine Environments

Taiwan is an island with a humid subtropical climate. The relatively warm seawater results in biofouling of the surfaces of marine facilities. Biocide application is a common practice for combating and eliminating adhesive fouling. However, a single type of biocide may have limited antimicrobial effects due to the relatively high microbial diversity in marine environments. Therefore, applying a mixture of various biocides may be necessary. In this study, the antimicrobial and anticorrosion properties of a newly designed composite biocide, namely a combination of thymol and benzyldimethyldodecylammonium chloride, were investigated by applying the biocide to 304 stainless steel substrates immersed in inocula containing bacterial strains from Tamsui and Zuoying harbors. The ability of 3TB and 5TB treatments to prevent sessile cells and biofilm formation on the 304 stainless steel coupon surface was determined through scanning electron microscopy investigation. In addition, confocal laser scanning microscopy indicated that the 5TB treatment achieved a greater bactericidal effect in both the Tamsui and Zuoying inocula. Moreover, electrochemical impedance spectroscopy revealed that the diameter of the Nyquist semicircle was almost completely unaffected by Tamsui or Zuoying under the 5TB treatment. Through these assessments of antimicrobial activity and corrosion resistance, 5TB treatment was demonstrated to have superior bactericidal activity against mixed strains in both southern and northern Taiwanese marine environments.

The hydrogen threshold of obligately methyl-reducing methanogens

Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures < 0.1 Pa, which is almost one order of magnitude lower than the thresholds for M. stadtmanae and M. blatticola reported in the only previous study on this topic. We conclude that methylotrophic methanogens should outcompete hydrogenotrophic methanogens for hydrogen and that their activity is limited by the availability of methyl groups.

Sulfate and metal removal from acid mine drainage using sugarcane vinasse as electron donor: Performance and microbial community of the down-flow structured-bed bioreactor

The down flow structured bed bioreactor (DFSBR) was applied to treat synthetic acid mine drainage (AMD) to reduce sulfate, increase the pH and precipitate metals in solutions (Co, Cu, Fe, Mn, Ni and Zn) using vinasse as an electron donor for sulfate-reducing bacteria (SRB). DFSBR achieved sulfate removal efficiencies between 55 and 91%, removal of Co and Ni were obtained with efficiencies greater than 80%, while Fe, Zn, Cu and Mn were removed with average efficiencies of 70, 80, 73 and 60%, respectively. Sulfate reduction increased pH from moderately acidic to 6.7-7.5. Modelling data confirmed the experimental results and metal sulfide precipitation was the mainly responsible for metal removal. The main genera responsible for sulfate and metal reduction were Geobacter and Desulfovibrio while fermenters were Parabacteroides and Sulfurovum. Moreover, in syntrophism with SRB, they played an important role in the efficiency of metal and sulfate removal.

Anaerobic microbial methanol conversion in marine sediments

Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.

Mechanistic insights into the effect of poly ferric sulfate on anaerobic digestion of waste activated sludge

Poly ferric sulfate (PFS), one of the typical inorganic flocculants widely used in wastewater management and waste activated sludge (WAS) dewatering, could be accumulated in WAS and inevitably entered in anaerobic digestion system at high levels. However, knowledge about its impact on methane production is virtually absent. This study therefore aims to fill this gap and provide insights into the mechanisms involved through both batch and long-term tests using either real WAS or synthetic wastewaters as the digestion substrates. Experimental results showed that the maximum methane potential and production rate of WAS was respectively retarded by 39.0% and 66.4%, whereas the lag phase was extended by 237.0% at PFS of 40 g per kg of total solids. Mechanism explorations exhibited that PFS induced the physical enmeshment and disrupted the enzyme activity involved in anaerobic digestion, resulting in an inhibitory state of the bioprocess of hydrolysis, acidogenesis, and methanogenesis. Furthermore, PFS's inhibition to hydrogenotrophic methanogenesis was much severer than that to acetotrophic methanogenesis, which could be supported by the elevated abundances of Methanosaeta sp and the dropped abundances of Methanobacterium sp in PFS-present digester, and probably due to the severe mass transfer resistance of hydrogen between the syntrophic bacteria and methanogens, as well as the higher hydrogen appetency of PFS-induced sulfate reducing bacteria. Among the derivatives of PFS, "multinucleate and multichain-hydroxyl polymers" and sulfate were unveiled to be the major contributors to the decreased methane potential, while the "multinucleate and multichain-hydroxyl polymers" were identified to be the chief buster to the slowed methane-producing rate and the extended lag time.

Effect of Temperature on Acetate Mineralization Kinetics and Microbial Community Composition in a Hydrocarbon-Affected Microbial Community During a Shift From Oxic to Sulfidogenic Conditions

Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with ¹³C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.

Inhibition mitigation of methanogenesis processes by conductive materials: A critical review

Methanogenesis can be promoted by the addition of conductive materials. Although stimulating effects of conductive materials on methane (CH₄) production has been extensively reported, the crucial roles on recovering methanogenic activities under inhibitory conditions have not been systematically discussed. This critical review presents the current findings on the effects of conductive materials in methanogenic systems under volatile fatty acids (VFAs), ammonia, sulfate, and nano-cytotoxicity stressed conditions. Conductive materials induce fast VFAs degradation, avoiding VFAs accumulation during anaerobic digestion. Under high ammonia concentrations, conductive materials may ensure sufficient energy conservation for methanogens to maintain intracellular pH and proton balance. When encountering the competition of sulfate-reducing bacteria, conductive materials can benefit electron competitive capability of methanogens, recovering CH₄ production activity. Conductive nanomaterials stimulate the excretion of extracellular polymeric substances, which can prevent cells from nano-cytotoxicity. Future perspectives about unraveling mitigation mechanisms induced by conductive materials in methanogenesis processes are further discussed.

Effect of Sub-Stoichiometric Fe(III) Amounts on LCFA Degradation by Methanogenic Communities

Long-chain fatty acids (LCFA) are common contaminants in municipal and industrial wastewater that can be converted anaerobically to methane. A low hydrogen partial pressure is required for LCFA degradation by anaerobic bacteria, requiring the establishment of syntrophic relationships with hydrogenotrophic methanogens. However, high LCFA loads can inhibit methanogens, hindering biodegradation. Because it has been suggested that anaerobic degradation of these compounds may be enhanced by the presence of alternative electron acceptors, such as iron, we investigated the effect of sub-stoichiometric amounts of Fe(III) on oleate (C18:1 LCFA) degradation by suspended and granular methanogenic sludge. Fe(III) accelerated oleate biodegradation and hydrogenotrophic methanogenesis in the assays with suspended sludge, with H₂-consuming methanogens coexisting with iron-reducing bacteria. On the other hand, acetoclastic methanogenesis was delayed by Fe(III). These effects were less evident with granular sludge, possibly due to its higher initial methanogenic activity relative to suspended sludge. Enrichments with close-to-stoichiometric amounts of Fe(III) resulted in a microbial community mainly composed of Geobacter, Syntrophomonas, and Methanobacterium genera, with relative abundances of 83-89%, 3-6%, and 0.2-10%, respectively. In these enrichments, oleate was biodegraded to acetate and coupled to iron-reduction and methane production, revealing novel microbial interactions between syntrophic LCFA-degrading bacteria, iron-reducing bacteria, and methanogens.

Root microbiomes as indicators of seagrass health

The development of early warning indicators that identify ecosystem stress is a priority for improving ecosystem management. As microbial communities respond rapidly to environmental disturbance, monitoring their composition could prove one such early indicator of environmental stress. We combined 16S rRNA gene sequencing of the seagrass root microbiome of Halophila ovalis with seagrass health metrics (biomass, productivity and Fsulphide) to develop microbial indicators for seagrass condition across the Swan-Canning Estuary and the Leschenault Estuary (south-west Western Australia); the former had experienced an unseasonal rainfall event leading to declines in seagrass health. Microbial indicators detected sites of potential stress that other seagrass health metrics failed to detect. Genera that were more abundant in 'healthy' seagrasses included putative methylotrophic bacteria (e.g. Methylotenera and Methylophaga), iron cycling bacteria (e.g. Deferrisoma and Geothermobacter) and N2 fixing bacteria (e.g. Rhizobium). Conversely, genera that were more abundant in 'stressed' seagrasses were dominated by putative sulphur-cycling bacteria, both sulphide-oxidising (e.g. Candidatus Thiodiazotropha and Candidatus Electrothrix) and sulphate-reducing (e.g. SEEP-SRB1, Desulfomonile and Desulfonema). The sensitivity of the microbial indicators developed here highlights their potential to be further developed for use in adaptive seagrass management, and emphasises their capacity to be effective early warning indicators of stress.

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD)

Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.

New bacterial and archaeal lineages discovered in organic rich sediments of a large tropical Bay

The nutrient and oxygen gradient present in marine sediments promotes high levels of microbial diversity. We applied metagenomics and biogeochemical tools to analyze microbial communities in different sediment depths (0-4 m below sea floor, mbsf) from Guanabara Bay, Brazil, a brackish tropical ecosystem with a history of massive anthropogenic impacts, and a largely unknown sediment microbial diversity. Methanogens (e.g. Methanosarcinales, Methanomicrobiales) were more abundant at 1 mbsf, while sulphate-reducing microbes (Desulfurococcales, Thermoprotales, and Sulfolobales) were more abundant at deeper layers (4 mbsf; corresponding to 3 K Radiocarbon years before present, Holocene Epoch). Taxonomic analyzes and functional gene identification associated with anaerobic methane oxidation (e.g. monomethylamine methyltransferase (mtmB), trimethylamine methyltransferase (mttB) and CO dehydrogenase/acetyl-CoA synthase delta subunit) and sulfate reduction indicated the dominance of Campylobacteria (Sulfurimonas) at deeper sediment layers. Gene sequences related to assimilation of inorganic sulfur increased with depth, while organic sulfur related sequences decrease, accompanying the clear reduction in the concentration of sulfur, organic carbon and chla torwards deeper layers. Analyzes of metagenome assembled genomes also led to the discovery of a novel order within the phylum Acidobacteriota, named Guanabacteria. This novel order had several in silico phenotyping features that differentiate it from closely related phylogenetic neighbors (e.g. Acidobacteria, Aminicenantes, and Thermoanaerobaculum), including several genes (carbon monoxide dehydrogenase, CO dehydrogenase/CO-methylating acetyl-CoA synthase complex subunit beta, heterodisulfide reductase, sulfite exporter TauE/SafE family protein, sulfurtransferase) that relevant for the S and C cycles. Furthermore, the recovered Bathyarchaeota genome SS9 illustrates the methanogenic potential in deeper sediment layer.

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer

Methane-producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood. Here, we construct model synthetic communities using a sulfate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate. With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in the metabolism of these methanogens towards co-utilization of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities.

Sulfur Chemistry May Have Paved the Way for Evolution of Antioxidants

The first organisms on the young Earth, just 1-1.5 billion years old, were likely chemolithoautotrophic anaerobes, thriving in an anoxic world rich in water, CO₂, and N₂. It is generally assumed that, until the accumulation of O₂ in the atmosphere, life was exempted from the oxidative stress that reactive oxygen species (ROS) impose on hydrocarbon-based life. Therefore, it is perplexing to note that life on the early Earth already carried antioxidants such as superoxide dismutase enzymes, catalase, and peroxiredoxins, the function of which is to counteract all forms of ROS, including H₂O₂. Phylogenetic investigations suggest that the presence of these enzymes in the last universal common ancestor, far predating the great oxygenation event (GOE) sometime between 2.3 and 2.7 billion years ago, is thought to be due to the appearance of oxygen-producing microorganisms and the subsequent need to respond to the appearance of ROS. Since the metabolic enzymes that counteract ROS have been found in all domains of life, they are considered of primitive origin. Two questions arise: (1) Could there be a nonbiological source of ROS that predates the oxygenic microbial activity? (2) Could sulfur, the homologue of oxygen, have played that role? Reactive sulfur species (RSS) may have triggered the evolution of antioxidants such that the ROS antioxidants started out as "antisulfur" enzymes developed to cope with, and take advantage of, various forms of RSS that were abundantly present on the early Earth.

Ground food waste discharge to sewer enhances methane gas emission: A lab-scale investigation

Emission of sulfide and methane from sewerage system has been a major concern for a long time. Sewers are now facing emerging challenges, such as receiving food waste (FW) to relieve the burdens on solid waste treatment. However, the knowledge of the direct impact of FW addition on sulfide and methane production in and emission from sewers is still lacking. In this study, two lab-scale sewer reactors, one without and one with FW addition, were continuously operated to investigate the production of sulfide and methane and microbial communities arising from FW discharge to freshwater sewerage system. The 190-day long-term monitoring and the batch tests on days 69 and 124 suggest that the FW addition has little impact on sulfide production possibly due to the limited sulfate concentration (40 mg S/L) but enhanced methane production by up to 60%. Moreover, cryosection-fluorescence in situ hybridization (FISH) revealed that the FW addition significantly stimulated the accumulation of methanogenic archaea (MA) in sewer biofilms and altered the spatial distributions of sulfate-reducing bacteria (SRB) and MA. Moreover, the relative abundance of MA in biofilms with FW addition was higher than that without FW addition, whereas the relative abundance of SRB was similar. Metabolic pathway analysis for sulfidogenesis and methanogenesis indicates that sufficient substrates derived from the FW addition were biodegraded during fermentation to produce acetate and hydrogen, and consequently facilitate methanogenesis. These findings shed light on the impacts of changes in wastewater compositions (e.g., FW addition) on sulfide and methane production in the freshwater sewerage system for improved policy-making on sewer management.

Industrial wastes: Fly ash, steel slag and phosphogypsum- potential candidates to mitigate greenhouse gas emissions from paddy fields

Waste management and global warming are the two challenging issues of the present global scenario. Increased human population has set the platform for rapid industrialization and modern agriculture. The industries such as energy, steel, and fertilizers play a significant role in improving the social, and economic status of human beings. The industrial production of energy (that involves combustion of coal), production of steel items and diammonium ammonium fertilizer generate a huge amount of wastes such as fly ash (FA), steel slag (SS) and phosphogypsum (PG), respectively. Inappropriate dumping of any kind of waste poses a threat to the environment, therefore, scientific management of waste is required to reduce associated environmental risks. These wastes i.e. SS, FA, and PG being rich sources of oxides of calcium (CaO), silicon (SiO₂), iron (FeO), and aluminum (Al₂O₃), etc. may affect the release of greenhouse gases from the soil. The information associated with the application of FA, SS, and PG onto the paddy fields and their impacts on methane and nitrous oxide emissions are highly fragmented and scarce. The present review extensively and critically explores the available information with respect to the effective utilization of FA, SS, and PG in paddy cultivation, their potential to mitigate greenhouse gases emission and their associated mechanisms. The fine grid assessment of these waste management provides new insight into the next level research and future policy options for industries and farmers.

Sulfate in anaerobic co-digester accelerates methane production from food waste and waste activated sludge

The presence of sulfate in food waste (FW) and waste activated sludge (WAS) threatens the anaerobic co-digestion for methane production. In this study, methane production from the anaerobic co-digestion of FW and WAS at sulfate concentrations of 50, 100, and 400 mg S/L was not affected, but instead deteriorated at 200 and 300 mg S/L. However, a model-based kinetic analysis reveals that sulfate can significantly promote the conversion of rapidly biodegradable substrates by up to 93%. From a point of thermodynamic view, the presence of sulfate can stimulate sulfate-reducing bacteria acting as acetogens to convert propionate to acetate, providing an alternative metabolic pathway for methanogenesis. In the anaerobic co-digestion, regulation of sulfate can be a potential strategy to improve the efficiency of methane production. However, more research is needed to optimize the sulfate concentration and substrate types in the anaerobic co-digester.

Complementary DNA/RNA-Based Profiling: Characterization of Corrosive Microbial Communities and Their Functional Profiles in an Oil Production Facility

DNA and RNA-based sequencing of the 16S rRNA gene and transcripts were used to assess the phylogenetic diversity of microbial communities at assets experiencing corrosion in an oil production facility. The complementary methodological approach, coupled with extensive bioinformatics analysis, allowed to visualize differences between the total and potentially active communities present in several locations of the production facility. According to the results, taxa indicative for thermophiles and oil-degrading microorganisms decreased their relative abundances in the active communities, whereas sulfate reducing bacteria and methanogens had the opposite pattern. The differences in the diversity profile between total and active communities had an effect on the microbial functional capability predicted from the 16S rRNA sequences. Primarily, genes involved in methane metabolism were enriched in the RNA-based sequencing approach. Comparative analysis of microbial communities in the produced water, injection water and deposits in the pipelines showed that deposits host more individual species than other sample sources in the facility. Similarities in the number of cells and microbial profiles of active communities in biocide treated and untreated sampling locations suggested that the treatment was ineffective at controlling the growth of microbial populations with a known corrosive metabolism. Differences in the results between DNA and RNA-based profiling demonstrated that DNA results alone can lead to the underestimation of active members in the community, highlighting the importance of using a complementary approach to obtain a broad general overview not only of total and active members but also in the predicted functionality.

A novel carbon monoxide fed moving bed biofilm reactor for sulfate rich wastewater treatment

In this study, a moving bed biofilm reactor was used for biodesulfuruization using CO as the sole carbon substrate. The effect of hydraulic retention time (HRT), sulfate loading rate and CO loading rate on sulfate and CO removal was examined. At 72, 48 and 24 h HRT, the sulfate removal was 93.5%, 91.9% and 80.1%, respectively. An increase in the sulfate loading reduced the sulfate reduction efficiency, which, however, was improved by increasing the CO flow rate into the MBBR. Best results in terms of sulfate reduction (>80%) were obtained for low inlet sulfate and high CO loading conditions. The CO utilization was very high at 85% throughout the study, except during the last phase of the continuous bioreactor operation it was around 70%. An artificial neural network based model was successfully developed and optimized to accurately predict the bioreactor performance in terms of both sulfate reduction and CO utilization. Overall, this study showed an excellent potential of the moving bed biofilm bioreactor for efficient sulfate reduction even under high loading conditions.

Biological pretreatment enhances the activity of functional microorganisms and the ability of methanogenesis during anaerobic digestion

Biological pretreatment can increase the methane production of anaerobic digestion. In this study, stover was pretreated via microbial consortium prior to anaerobic digestion; through 16S rRNA gene and 16S rRNA amplicon sequencing and metatranscriptomic analysis, and the effects of the pretreatment on the microbial community and critical factors of the increased methane production were studied. Microbial community structure was less affected by the pretreatment, which ensures the stable performance of anaerobic digestion. The methane production increased by 62.85% at the peak phase compared to the untreated stover. The activity of Methanosaeta increased from 2.0% to 10.1%, significantly enhancing the ability of the community to capture acetic acid and reduce CO₂ to methane. The main contribution to the increase in methane production was a unique acetyl-CoA synthetase, which showed significant up-regulation (121.8%). This research demonstrated the importance of Methanosaeta and its unique metabolic pathways in anaerobic digestion utilizing a biological pretreatment.

Anaerobic Dechlorination by a Humin-Dependent Pentachlorophenol-Dechlorinating Consortium under Autotrophic Conditions Induced by Homoacetogenesis

Anoxic aquifers suffer from energy limitations due to the unavailability of organic substrates, as dictated by hydrogen (H2) for various electron-accepting processes. This deficiency often results in the accumulation of persistent organic pollutants, where bioremediation using organic compounds often leads to secondary contamination. This study involves the reductive dechlorination of pentachlorophenol (PCP) by dechlorinators that do not use H2 directly, but rather through a reduced state of humin-a solid-phase humic substance-as the extracellular electron donor, which requires an organic donor such as formate, lactate, etc. This shortcoming was addressed by the development of an anaerobic mixed culture that was capable of reductively dechlorinating PCP using humin under autotrophic conditions induced by homoacetogenesis. Here, H2 was used for carbon-dioxide fixation to acetate; the acetate produced was used for the reduction of humin; and consequently used for dechlorination through reduced humin. The 16SrRNA gene sequencing analysis showed Dehalobacter and Dehalobacterium as the possible dechlorinators, while Clostridium and Oxobacter were identified as the homoacetogens. Thus, this work contributes to the development of an anaerobic consortium that balanced H2 dependency, where efficiency of humin reduction extends the applicability of anaerobic microbial remediation in aquifers through autotrophy, syntrophy, and reductive dechlorination.

Simultaneous production of methane and acetate by thermophilic mixed culture from carbon dioxide in bioelectrochemical system

A thermophilic bioelectrochemical system was operated with mixed culture at 60 °C, while introducing only carbon dioxide. Methane production was initially observed in a membrane-less single chamber without a mediator, but eventually acetate was also found as 10.5 g/L after 137 days of operation. Comparing the microbial communities before and after the electricity supply using next-generation sequencing technology, acetoclastic methanogens such as Methanosaeta concilii were increased, and this result also indicates the production of acetate in bioelectrochemical CO₂ conversion system. With the advent of sulfate-reducing bacteria, Desulfotomaculum peckii was considered to be an acetate production promoter. These high production results for both methane and acetate can be applied to CO₂ storage using excess electricity for value-added chemicals.

Wetland Sediments Host Diverse Microbial Taxa Capable of Cycling Alcohols

Understanding patterns of organic matter degradation in wetlands is essential for identifying the substrates and mechanisms supporting greenhouse gas production and emissions from wetlands, the main natural source of methane in the atmosphere. Alcohols are common fermentation products but are poorly studied as key intermediates in organic matter degradation in wetlands. By investigating genes, pathways, and microorganisms potentially accounting for the high concentrations of ethanol and isopropanol measured in Prairie Pothole wetland sediments, this work advanced our understanding of alcohol fermentations in wetlands linked to extremely high greenhouse gas emissions. Moreover, the novel alcohol dehydrogenases and microbial taxa potentially involved in alcohol metabolism may serve biotechnological efforts in bioengineering commercially valuable alcohol production and in the discovery of novel isopropanol producers or isopropanol fermentation pathways.

Alcohols are commonly derived from the degradation of organic matter and yet are rarely measured in environmental samples. Wetlands in the Prairie Pothole Region (PPR) support extremely high methane emissions and the highest sulfate reduction rates reported to date, likely contributing to a significant proportion of organic matter mineralization in this system. While ethanol and isopropanol concentrations up to 4 to 5 mM in PPR wetland pore fluids have been implicated in sustaining these high rates of microbial activity, the mechanisms that support alcohol cycling in this ecosystem are poorly understood. We leveraged metagenomic and transcriptomic tools to identify genes, pathways, and microorganisms potentially accounting for alcohol cycling in PPR wetlands. Phylogenetic analyses revealed diverse alcohol dehydrogenases and putative substrates. Alcohol dehydrogenase and aldehyde dehydrogenase genes were included in 62 metagenome-assembled genomes (MAGs) affiliated with 16 phyla. The most frequently encoded pathway (in 30 MAGs) potentially accounting for alcohol production was a Pyrococcus furiosus-like fermentation which can involve pyruvate:ferredoxin oxidoreductase (PFOR). Transcripts for 93 of 137 PFOR genes in these MAGs were detected, as well as for 158 of 243 alcohol dehydrogenase genes retrieved from these same MAGs. Mixed acid fermentation and heterofermentative lactate fermentation were also frequently encoded. Finally, we identified 19 novel putative isopropanol dehydrogenases in 15 MAGs affiliated with Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Ignavibacteriae, Thaumarchaeota, and the candidate divisions KSB1 and Rokubacteria. We conclude that diverse microorganisms may use uncommon and potentially novel pathways to produce ethanol and isopropanol in PPR wetland sediments.

IMPORTANCE Understanding patterns of organic matter degradation in wetlands is essential for identifying the substrates and mechanisms supporting greenhouse gas production and emissions from wetlands, the main natural source of methane in the atmosphere. Alcohols are common fermentation products but are poorly studied as key intermediates in organic matter degradation in wetlands. By investigating genes, pathways, and microorganisms potentially accounting for the high concentrations of ethanol and isopropanol measured in Prairie Pothole wetland sediments, this work advanced our understanding of alcohol fermentations in wetlands linked to extremely high greenhouse gas emissions. Moreover, the novel alcohol dehydrogenases and microbial taxa potentially involved in alcohol metabolism may serve biotechnological efforts in bioengineering commercially valuable alcohol production and in the discovery of novel isopropanol producers or isopropanol fermentation pathways.

Thinking Outside the Cereal Box: Noncarbohydrate Routes for Dietary Manipulation of the Gut Microbiota

The gut microbiota is a diverse and dynamic ecological community that is increasingly recognized to play important roles in host metabolic, immunological, and behavioral functioning. As such, identifying new routes for manipulating the microbiota may provide valuable additional methods for improving host health. Dietary manipulations and prebiotic supplementation are active targets of research for altering the microbiota, but to date, this work has disproportionately focused on carbohydrates. However, many other resources can limit or shape microbial growth. Here, we provide a brief overview of the resource landscape in the mammalian gut and review relevant literature documenting associations between noncarbohydrate nutrients and the composition of the gut microbiota. To spur future work and accelerate translational applications, we propose that researchers take new approaches for studying the effects of diet on gut microbial communities, including more-careful consideration of media for in vitro experiments, measurement of absolute as well as relative abundances, concerted efforts to articulate how physiology may differ between humans and the animal models used in translational studies, and leveraging natural variation for additional insights. Finally, we close with a discussion of how to determine when or where to employ these potential dietary levers for manipulating the microbiota.

Formation of Large Native Sulfur Deposits Does Not Require Molecular Oxygen

Large native (i.e., elemental) sulfur deposits can be part of caprock assemblages found on top of or in lateral position to salt diapirs and as stratabound mineralization in gypsum and anhydrite lithologies. Native sulfur is formed when hydrocarbons come in contact with sulfate minerals in presence of liquid water. The prevailing model for native sulfur formation in such settings is that sulfide produced by sulfate-reducing bacteria is oxidized to zero-valent sulfur in presence of molecular oxygen (O2). Although possible, such a scenario is problematic because: (1) exposure to oxygen would drastically decrease growth of microbial sulfate-reducing organisms, thereby slowing down sulfide production; (2) on geologic timescales, excess supply with oxygen would convert sulfide into sulfate rather than native sulfur; and (3) to produce large native sulfur deposits, enormous amounts of oxygenated water would need to be brought in close proximity to environments in which ample hydrocarbon supply sustains sulfate reduction. However, sulfur stable isotope data from native sulfur deposits emplaced at a stage after the formation of the host rocks indicate that the sulfur was formed in a setting with little solute exchange with the ambient environment and little supply of dissolved oxygen. We deduce that there must be a process for the formation of native sulfur in absence of an external oxidant for sulfide. We hypothesize that in systems with little solute exchange, sulfate-reducing organisms, possibly in cooperation with other anaerobic microbial partners, drive the formation of native sulfur deposits. In order to cope with sulfide stress, microbes may shift from harmful sulfide production to non-hazardous native sulfur production. We propose four possible mechanisms as a means to form native sulfur: (1) a modified sulfate reduction process that produces sulfur compounds with an intermediate oxidation state, (2) coupling of sulfide oxidation to methanogenesis that utilizes methylated compounds, acetate or carbon dioxide, (3) ammonium oxidation coupled to sulfate reduction, and (4) sulfur comproportionation of sulfate and sulfide. We show these reactions are thermodynamically favorable and especially useful in environments with multiple stressors, such as salt and dissolved sulfide, and provide evidence that microbial species functioning in such environments produce native sulfur. Integrating these insights, we argue that microbes may form large native sulfur deposits in absence of light and external oxidants such as O2, nitrate, and metal oxides. The existence of such a process would not only explain enigmatic occurrences of native sulfur in the geologic record, but also provide an explanation for cryptic sulfur and carbon cycling beneath the seabed.

Rare Biosphere Archaea Assimilate Acetate in Precambrian Terrestrial Subsurface at 2.2 km Depth

The deep biosphere contains a large portion of the total microbial communities on Earth, but little is known about the carbon sources that support deep life. In this study, we used Stable Isotope Probing (SIP) and high throughput amplicon sequencing to identify the acetate assimilating microbial communities at 2260 m depth in the bedrock of Outokumpu, Finland. The long-term and short-term effects of acetate on the microbial communities were assessed by DNA-targeted SIP and RNA targeted cell activation. The microbial communities reacted within hours to the amended acetate. Archaeal taxa representing the rare biosphere at 2260 m depth were identified and linked to the cycling of acetate, and were shown to have an impact on the functions and activity of the microbial communities in general through small key carbon compounds. The major archaeal lineages identified to assimilate acetate and metabolites derived from the labelled acetate were Methanosarcina spp., Methanococcus spp., Methanolobus spp., and unclassified Methanosarcinaceae. These archaea have previously been detected in the Outokumpu deep subsurface as minor groups. Nevertheless, their involvement in the assimilation of acetate and secretion of metabolites derived from acetate indicated an important role in the supporting of the whole community in the deep subsurface, where carbon sources are limited.

Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea

A central goal in marine microecology is to understand the ecological factors shaping spatiotemporal microbial patterns and the underlying processes. We hypothesized that abiotic and/or biotic interactions are probably more important for explaining the distribution patterns of marine bacterioplankton than environmental filtering. In this study, surface seawater samples were collected about 7000 miles from the Mediterranean Sea, transecting the North Atlantic Ocean, to the Brazilian marginal sea. In bacterial biosphere, SAR11, SAR86, Rhodobacteraceae, and Rhodospiriaceae were predominant in the Mediterranean Sea; Prochlorococcus was more frequent in Atlantic Ocean; whereas in the Brazilian coastal sea, the main bacterial members were Synechococcus and SAR11. With respect to archaea, Euryarchaeota were predominant in the Atlantic Ocean and Thaumarchaeota in the Mediterranean Sea. With respect to the eukaryotes, Syndiniales, Spumellaria, Cryomonadida, and Chlorodendrales were predominant in the open ocean, while diatoms and microzooplankton were dominant in the coastal sea. Distinct clusters of prokaryotes and eukaryotes displayed clear spatial heterogeneity. Among the environmental parameters measured, temperature and salinity were key factors controlling bacterial and archaeal community structure, respectively, whereas N/P/Si contributed to eukaryotic variation. The relative contribution of environmental parameters to the microbial distribution pattern was 45.2%. Interaction analysis showed that Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the keystone taxa within the positive-correlation network, while Thermoplasmata was the main contributor in the negative-correlation network. Our study demonstrated that microbial communities are co-governed by environmental filtering and biotic interactions, which are the main deterministic driving factors modulating the spatiotemporal patterns of marine plankton synergistically at the regional or global levels.

Conductive Particles Enable Syntrophic Acetate Oxidation between Geobacter and Methanosarcina from Coastal Sediments

Coastal sediments are rich in conductive particles, possibly affecting microbial processes for which acetate is a central intermediate. In the methanogenic zone, acetate is consumed by methanogens and/or syntrophic acetate-oxidizing (SAO) consortia. SAO consortia live under extreme thermodynamic pressure, and their survival depends on successful partnership. Here, we demonstrate that conductive particles enable the partnership between SAO bacteria (i.e., Geobacter spp.) and methanogens (Methanosarcina spp.) from the coastal sediments of the Bothnian Bay of the Baltic Sea. Baltic methanogenic sediments were rich in conductive minerals, had an apparent isotopic fractionation characteristic of CO₂-reductive methanogenesis, and were inhabited by Geobacter and Methanosarcina. As long as conductive particles were delivered, Geobacter and Methanosarcina persisted, whereas exclusion of conductive particles led to the extinction of Geobacter. Baltic Geobacter did not establish a direct electric contact with Methanosarcina, necessitating conductive particles as electrical conduits. Within SAO consortia, Geobacter was an efficient [¹³C]acetate utilizer, accounting for 82% of the assimilation and 27% of the breakdown of acetate. Geobacter benefits from the association with the methanogen, because in the absence of an electron acceptor it can use Methanosarcina as a terminal electron sink. Consequently, inhibition of methanogenesis constrained the SAO activity of Geobacter as well. A potential benefit for Methanosarcina partnering with Geobacter is that together they competitively exclude acetoclastic methanogens like Methanothrix from an environment rich in conductive particles. Conductive particle-mediated SAO could explain the abundance of acetate oxidizers like Geobacter in the methanogenic zone of sediments where no electron acceptors other than CO₂ are available.

Acetate-oxidizing bacteria are known to thrive in mutualistic consortia in which H₂ or formate is shuttled to a methane-producing Archaea partner. Here, we discovered that such bacteria could instead transfer electrons via conductive minerals. Mineral SAO (syntrophic acetate oxidation) could be a vital pathway for CO₂-reductive methanogenesis in the environment, especially in sediments rich in conductive minerals. Mineral-facilitated SAO is therefore of potential importance for both iron and methane cycles in sediments and soils. Additionally, our observations imply that agricultural runoff or amendments with conductive chars could trigger a significant increase in methane emissions.

Control on rate and pathway of anaerobic organic carbon degradation in the seabed

The degradation of organic matter in the anoxic seabed proceeds through a complex microbial network in which the terminal steps are dominated by oxidation with sulfate or conversion into methane and CO₂ The controls on pathway and rate of the degradation process in different geochemical zones remain elusive. Radiotracer techniques were used to perform measurements of sulfate reduction, methanogenesis, and acetate oxidation with unprecedented sensitivity throughout Holocene sediment columns from the Baltic Sea. We found that degradation rates transition continuously from the sulfate to the methane zone, thereby demonstrating that terminal steps do not exert feedback control on upstream hydrolytic and fermentative processes, as previously suspected. Acetate was a key intermediate for carbon mineralization in both zones. However, acetate was not directly converted into methane. Instead, an additional subterminal step converted acetate to CO₂ and reducing equivalents, such as H₂, which then fed autotrophic reduction of CO₂ to methane.

Responses of Microbial Community Composition to Temperature Gradient and Carbon Steel Corrosion in Production Water of Petroleum Reservoir

Oil reservoir production systems are usually associated with a temperature gradient and oil production facilities frequently suffer from pipeline corrosion failures. Both bacteria and archaea potentially contribute to biocorrosion of the oil production equipment. Here the response of microbial populations from the petroleum reservoir to temperature gradient and corrosion of carbon steel coupons were investigated under laboratory condition. Carbon steel coupons were exposed to production water from a depth of 1809 m of Jiangsu petroleum reservoir (China) and incubated for periods of 160 and 300 days. The incubation temperatures were set at 37, 55, and 65°C to monitoring mesophilic, thermophilic and hyperthermophilic microorganisms associated with anaerobic carbon steel corrosion. The results showed that corrosion rate at 55°C (0.162 ± 0.013 mm year^-1) and 37°C (0.138 ± 0.008 mm year^-1) were higher than that at 65°C (0.105 ± 0.007 mm year^-1), and a dense biofilm was observed on the surface of coupons under all biotic incubations. The microbial community analysis suggests a high frequency of bacterial taxa associated with families Porphyromonadaceae, Enterobacteriaceae, and Spirochaetaceae at all three temperatures. While the majority of known sulfate-reducing bacteria, in particular Desulfotignum, Desulfobulbus and Desulfovibrio spp., were predominantly observed at 37°C; Desulfotomaculum spp., Thermotoga spp. and Thermanaeromonas spp. as well as archaeal members closely related to Thermococcus and Archaeoglobus spp. were substantially enriched at 65°C. Hydrogenotrophic methanogens of the family Methanobacteriaceae were dominant at both 37 and 55°C; acetoclastic Methanosaeta spp. and methyltrophic Methanolobus spp. were enriched at 37°C. These observations show that temperature changes significantly alter the microbial community structure in production fluids and also affected the biocorrosion of carbon steel under anaerobic conditions.

Qualitative Analysis of Microbial Dynamics during Anaerobic Digestion of Microalgal Biomass in a UASB Reactor

Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the data revealed that samples taken at different stages of AD had varying bacterial composition. A group consisting of Bacteroidales, Pseudomonadales, and Enterobacteriales was identified to be putatively responsible for the hydrolysis of microalgal biomass. The methanogenesis phase was dominated by Methanosarcina mazei. Results of observed changes in the composition of microbial communities during AD can be used as a road map to stimulate key bacterial species identified at each phase of AD to increase yield of biogas and rate of substrate decomposition. This research demonstrates a successful exploitation of methane production from microalgae without any biomass pretreatment.

Microbial Community Structure and Functions in Ethanol-Fed Sulfate Removal Bioreactors for Treatment of Mine Water

Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L⁻¹ sulfate, using granular sludge from an industrial waste water treatment plant as inoculum. The pH, redox potential, and sulfate and sulfide concentrations were measured twice a week over a maximum of 171 days. The microbial communities in the bioreactors were characterized by qPCR and high throughput amplicon sequencing. The pH in the bioreactors fluctuated between 5.0 and 7.7 with the highest amount of up to 50% sulfate removed measured around pH 6. Dissimilatory sulfate reducing bacteria (SRB) constituted only between 1% and 15% of the bacterial communities. Predicted bacterial metagenomes indicated a high prevalence of assimilatory sulfate reduction proceeding to formation of l-cystein and acetate, assimilatory and dissimilatory nitrate reduction, denitrification, and oxidation of ethanol to acetaldehyde with further conversion to ethanolamine, but not to acetate. Despite efforts to maintain optimal conditions for biological sulfate reduction in the bioreactors, only a small part of the microorganisms were SRB. The microbial communities were highly diverse, containing bacteria, archaea, and fungi, all of which affected the overall microbial processes in the bioreactors. While it is important to monitor specific physicochemical parameters in bioreactors, molecular assessment of the microbial communities may serve as a tool to identify biological factors affecting bioreactor functions and to optimize physicochemical attributes for ideal bioreactor performance.

Coexistence and competition of sulfate-reducing and methanogenic populations in an anaerobic hexadecane-degrading culture

BACKGROUND

Over three-fifths of the world's known crude oil cannot be recovered using state-of-the-art techniques, but microbial conversion of petroleum hydrocarbons trapped in oil reservoirs to methane is one promising path to increase the recovery of fossil fuels. The process requires cooperation between syntrophic bacteria and methanogenic archaea, which can be affected by sulfate-reducing prokaryotes (SRPs). However, the effects of sulfate on hydrocarbon degradation and methane production remain elusive, and the microbial communities involved are not well understood.

RESULTS

In this study, a methanogenic hexadecane-degrading enrichment culture was treated with six different concentrations of sulfate ranging from 0.5 to 25 mM. Methane production and maximum specific methane production rate gradually decreased to 44 and 56% with sulfate concentrations up to 25 mM, respectively. There was a significant positive linear correlation between the sulfate reduction/methane production ratio and initial sulfate concentration, which remained constant during the methane production phase. The apparent methanogenesis fractionation factor (αapp) gradually increased during the methane production phase in each treatment, the αapp for the treatments with lower sulfate (0.5-4 mM) eventually plateaued at ~1.047, but that for the treatment with 10-25 mM sulfate only reached ~1.029. The relative abundance levels of Smithella and Methanoculleus increased almost in parallel with the increasing sulfate concentrations. Furthermore, the predominant sulfate reducer communities shifted from Desulfobacteraceae in the low-sulfate cultures to Desulfomonile in the high-sulfate cultures.

CONCLUSION

The distribution of hexadecane carbon between methane-producing and sulfate-reducing populations is dependent on the initial sulfate added, and not affected during the methane production period. There was a relative increase in hydrogenotrophic methanogenesis activity over time for all sulfate treatments, whereas the total activity was inhibited by sulfate addition. Both Smithella and Methanoculleus, the key alkane degraders and methane producers, can adapt to sulfate stress. Specifically, different SRP populations were stimulated at various sulfate concentrations. These results could help to evaluate interactions between sulfate-reducing and methanogenic populations during anaerobic hydrocarbon degradation in oil reservoirs.

Significant enhancement by biochar of caproate production via chain elongation

In this study, biochar was introduced into a chain elongation system to enhance the bioproduction of caproate and caprylate. The concentration of caproate increased to 21.1 g/L upon the addition of biochar, which is the highest level of caproate reported for such a system to date when ethanol was used as electron donor. The addition of biochar created a tougher system with more stable microorganism community structure for chain elongation, in which no obvious inhibition by products or substrates was observed, moreover, the lag phase was reduced 2.3-fold compared to the system without biochar. These reinforcement effect of biochar are attributed to the enhanced conductivity due to the significant enrichment of functional microorganisms via the microbial network surrounding smaller biochar particles, and via the adsorption on the rough surfaces or pores of larger particles, which facilitated electron transfer. Higher amounts of extracellular polymer substances and higher conductivity induced by biochar could contribute to the reinforcement effect in chain elongation.

Concurrent Methane Production and Oxidation in Surface Sediment from Aarhus Bay, Denmark

Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with 13C-CH4 to quantify CH4 turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH4 production and oxidation rates (>200 pmol cm-3 d-1) were found in the top 0-2 cm, below which rates dropped below 100 pmol cm-3 d-1 in all other segments down to 16 cm. This drop in overall methane turnover with depth was accompanied by decreasing rates of organic matter mineralization with depth. Molecular analyses based on quantitative PCR and MiSeq sequencing of archaeal 16S rRNA genes showed that the abundance of methanogenic archaea also peaked in the top 0-2 cm segment. Based on the community profiling, hydrogenotrophic and methylotrophic methanogens dominated among the methanogenic archaea in general, suggesting that methanogenesis in surface sediment could be driven by both CO2 reduction and fermentation of methylated compounds. Our results show the existence of elevated methanogenic activity and a dynamic recycling of CH4 at low concentration in sulfate-rich marine surface sediment. Considering the common environmental conditions found in other coastal systems, we speculate that such a cryptic methane cycling can be ubiquitous.

Co-existence of Methanogenesis and Sulfate Reduction with Common Substrates in Sulfate-Rich Estuarine Sediments

The competition between sulfate reducing bacteria and methanogens over common substrates has been proposed as a critical control for methane production. In this study, we examined the co-existence of methanogenesis and sulfate reduction with shared substrates over a large range of sulfate concentrations and rates of sulfate reduction in estuarine systems, where these processes are the key terminal sink for organic carbon. Incubation experiments were carried out with sediment samples from the sulfate-methane transition zone of the Yarqon (Israel) estuary with different substrates and inhibitors along a sulfate concentrations gradient from 1 to 10 mM. The results show that methanogenesis and sulfate reduction can co-exist while the microbes share substrates over the tested range of sulfate concentrations and at sulfate reduction rates up to 680 μmol L-1 day-1. Rates of methanogenesis were two orders of magnitude lower than rates of sulfate reduction in incubations with acetate and lactate, suggesting a higher affinity of sulfate reducing bacteria for the available substrates. The co-existence of both processes was also confirmed by the isotopic signatures of δ34S in the residual sulfate and that of δ13C of methane and dissolved inorganic carbon. Copy numbers of dsrA and mcrA genes supported the dominance of sulfate reduction over methanogenesis, while showing also the ability of methanogens to grow under high sulfate concentration and in the presence of active sulfate reduction.